Often I’d want to make parts of an object separately then merge them together. What I used to do was just combine them or use boolean operations, which either results in redundant faces or screwed up normals. Finally, I’ve learnt to do it properly by using the Append to Polygon Tool.
So here’s a hammer that I modelled to learn how to use the tool.
First I made the hammer in three parts using the usual extrude tool and manipulation handles. You can see that these are still separate objects because clicking on a part of the hammer doesn’t select the whole hammer.
Step one is to delete all the faces that you won’t need. I deleted four faces in total – 2 where the handle meets the head, and 2 where the tip meets the rest of the head.
Step two is to select the objects that you want to make as one and select Mesh –> Combine. (I tend to forget this step. If you don’t, you can’t append polygons between two objects.)
Select Edit Mesh –> Append to Polygon Tool. Now if you click on an edge where you want to create a face, magenta arrows appear. Keep clicking on edges in the direction of the arrows and hit Enter to close the face off. A preview of the new face will appear in pink as you click on edges.
You might need to divide it up and use the tool several times to make multiple faces so the hole gets filled in correctly.
If you do the same for the face to connect the handle and the head, the hammer will be one object that is connected properly. You can always use the Split Polygon Tool afterwards so that the polygons you created become quads or triangles.